Detection of acute HIV infections

Evaluating the efficiency of specimen pooling for PCR-based detection of COVID-19

In the age of a pandemic, such as the ongoing one caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the world faces a limited supply of tests, personal protective equipment, and factories and supply chains are struggling to meet the growing demands. This study aimed to evaluate the efficacy of specimen pooling for testing of SARS‐CoV‐2 virus, to determine whether costs and resource savings could be achieved without impacting the sensitivity of the testing. Ten previously tested nasopharyngeal and throat swab specimens by real‐time polymerase chain reaction (PCR), were pooled for testing, containing either one or two known positive specimens of varying viral concentrations. Specimen pooling did not affect the sensitivity of detecting SARS‐CoV‐2 when the PCR cycle threshold (Ct) of original specimen was lower than 35. In specimens with low viral load (Ct > 35), 2 of 15 pools (13.3%) were false negative. Pooling specimens to test for Coronavirus Disease 2019 infection in low prevalence (≤1%) areas or in low risk populations can dramatically decrease the resource burden on laboratory operations by up to 80%. This paves the way for large‐scale population screening, allowing for assured policy decisions by governmental bodies to ease lockdown restrictions in areas with a low incidence of infection, or with lower‐risk populations.

Specimen pooling did not affect the sensitivity of detecting SARS‐CoV.

Pooling specimens to test for COVID‐19 infection can dramatically decrease the resource burden on laboratory operations.

Specimen pooling in samples whose cycle threshold (Ct) value is greater than 35 may yield false‐negative results.

Pooling specimens is especially useful for large‐scale population screening.

No Time to Delay! Fiebig Stages and Referral in Acute HIV infection: Seattle Primary Infection Program Experience

There has been increasing recognition of the importance of diagnosing individuals during the earliest stages of human immunodeficiency virus (HIV) infection. Sera from individuals referred to a primary HIV infection research program were screened using the IgG-sensitive Vironostika HIV-1 Microelisa System, IgG/IgM-sensitive GS HIV-1/HIV-2 Plus O antibody enzyme immunoassay (EIA), or Abbott ARCHITECT HIV antigen (Ag)/antibody (Ab) Combo assay and confirmed by the Bio-Rad Multispot and Western blot. A subset of participants was co-enrolled in a study designed to compare the ability of point-of-care tests to detect early infection. We calculated time within primary infection laboratory stages using actual observed transitions and with an expectation-maximization algorithm. Three hundred and sixty participants contributed data to this analysis. Of 123 persons referred with EIA-negative/RNA-positive test results (Fiebig stage I-II) or for concern for symptoms, 24 (20%) were still in stages I-II, and 99 (80%) were in stages III or later at their screening visit. Participants were estimated to spend a median of 13.5 days in stages I and II, 2.3 days in stage III, and 7.8 days in stage IV. OraQuick performed on oral fluids detected 53% of 17 participants in stage V. The durations of stages we observed are consistent with previous publications. Most persons referred for research no longer had acute infection at their first visit. Programs wishing to identify persons in the very earliest stages of infection need to expedite referrals or develop targeted screening programs.

Clinical and public health implications of acute and early HIV detection and treatment: a scoping review

INTRODUCTION

The unchanged global HIV incidence may be related to ignoring acute HIV infection (AHI). This scoping review examines diagnostic, clinical, and public health implications of identifying and treating persons with AHI.

METHODS

We searched PubMed, in addition to hand-review of key journals identifying research pertaining to AHI detection and treatment. We focused on the relative contribution of AHI to transmission and the diagnostic, clinical, and public health implications. We prioritized research from low- and middle-income countries (LMICs) published in the last fifteen years.

RESULTS AND DISCUSSION

Extensive AHI research and limited routine AHI detection and treatment have begun in LMIC. Diagnostic challenges include ease-of-use, suitability for application and distribution in LMIC, and throughput for high-volume testing. Risk score algorithms have been used in LMIC to screen for AHI among individuals with behavioural and clinical characteristics more often associated with AHI. However, algorithms have not been implemented outside research settings. From a clinical perspective, there are substantial immunological and virological benefits to identifying and treating persons with AHI - evading the irreversible damage to host immune systems and seeding of viral reservoirs that occurs during untreated acute infection. The therapeutic benefits require rapid initiation of antiretrovirals, a logistical challenge in the absence of point-of-care testing. From a public health perspective, AHI diagnosis and treatment is critical to: decrease transmission via viral load reduction and behavioural interventions; improve pre-exposure prophylaxis outcomes by avoiding treatment initiation for HIV-seronegative persons with AHI; and, enhance partner services via notification for persons recently exposed or likely transmitting.

CONCLUSIONS

There are undeniable clinical and public health benefits to AHI detection and treatment, but also substantial diagnostic and logistical barriers to implementation and scale-up. Effective early ART initiation may be critical for HIV eradication efforts, but widespread use in LMIC requires simple and accurate diagnostic tools. Implementation research is critical to facilitate sustainable integration of AHI detection and treatment into existing health systems and will be essential for prospective evaluation of testing algorithms, point-of-care diagnostics, and efficacious and effective first-line regimens.

Detection of HIV RNA in dried blood spots and oral fluids

: We evaluated detection of HIV-1 RNA from dried blood spots (DBS) and oral fluid specimens. Between February 2010 and August 2014, HIV-1 was newly diagnosed in eight (2.6%) study participants who had median blood HIV-1 RNA of 61 500 copies/ml (interquartile range 7500-146 000). RNA was detected in seven (87.5%) DBS and three (37.5%) oral fluid swabs but was not detected in either specimen from one participant. DBS may be a reasonable specimen collection method to detect acute infection.

Differences in Risk Behavior and Demographic Factors Between Men Who Have Sex With Men With Acute and Nonacute Human Immunodeficiency Virus Infection in a Community-Based Testing Program in Los Angeles

INTRODUCTION

High viremia combined with HIV-infection status unawareness and increased sexual risk behavior contributes to a disproportionate amount of new HIV infections.

METHODS

From August 2011 to July 2015, the Los Angeles Lesbian, Gay, Bisexual, and Transgender Center conducted 66,546 HIV tests. We compared factors, including the presence of concomitant sexually transmitted infections, number of recent sex partners and reported condomless anal intercourse between men who have sex with men (MSM) diagnosed with an acute HIV infection and a nonacute HIV infection using multivariable logistic regression.

RESULTS

Of 1082 unique MSM who tested HIV-infected for the first time, 165 (15%) had an acute infection and 917 had a nonacute infection. HIV rapid antibody testing was 84.8% sensitive for detecting HIV infection (95% confidence interval (CI): 82.9% to 87.1%). Median HIV viral load among acutely infected MSM was 842,000 copies per milliliter (interquartile range = 98,200-4,897,318). MSM with acute infection had twice the number of sex partners in the prior 30 days (median = 2) and prior 3 months (median = 4) before diagnosis compared with those diagnosed with nonacute infection (P ≤ 0.0001). The odds of acute HIV infection were increased with the numbers of recent sex partners after controlling for age and race/ethnicity (adjusted odds ratio (aOR) >5 partners in past 30 days = 2.74; 95% CI: 1.46 to 5.14; aOR >10 partners in past 3 months = 2.41; 95% CI: 1.36 to 4.25). Non-African American MSM had almost double the odds of being diagnosed with an acute HIV infection compared with African American MSM (aOR = 1.97; 95% CI: 1.10 to 3.52).

CONCLUSIONS

MSM with acute HIV infection had nearly twice as many sex partners in the past 30 days and 3 months compared with MSM with newly diagnosed nonacute HIV infection. Those diagnosed with acute HIV infection had decreased odds of being African American MSM.

Performance of Determine Combo and other point-of-care HIV tests among Seattle MSM

BACKGROUND AND OBJECTIVE

The rapid test study was a real-time comparison of point-of-care (POC) HIV tests to determine their abilities to detect early HIV infection.

STUDY DESIGN

Men and transgender persons reporting sex with men in the prior year were recruited at the Public Health-Seattle & King County STD Clinic, Gay City Health Project, and University of Washington Primary Infection Clinic. Study tests included the OraQuick ADVANCE Rapid HIV-1/2 Antibody Test performed on oral fluids and tests performed on fingerstick whole blood specimens including OraQuick, Uni-Gold Recombigen HIV test, Determine HIV-1/2 Ag/Ab Combo, and INSTI HIV-1 Rapid Antibody Test. Specimens from subjects with negative results were sent for EIA and nucleic acid amplification testing. McNemar's exact tests compared the numbers of HIV-infected subjects detected.

RESULTS

Between February 2010 and August 2014, there were 3438 study visits. Twenty-four subjects had discordant POC results with at least one reactive and one non-reactive test, including one subject with a reactive Determine p24 antigen. OraQuick performed on oral fluids identified fewer persons compared to all fingerstick tests. OraQuick performed on fingerstick whole blood detected fewer persons compared to the Determine Combo antibody component (p=.008) and Combo overall (p=.004), and there was a trend when compared to INSTI (p=.06). The Determine Combo specificity was 98.99%.

CONCLUSIONS

As reported by others, Determine Combo underperforms compared to laboratory-based testing, but it did detect one acute infection. If these results are validated, the specificity of Determine Combo may limit its usefulness in populations with lower HIV incidence.

How can we better identify early HIV infections?

PURPOSE OF REVIEW

Detection of early HIV infections (EHIs), including acute HIV infection (AHI), is important for individual health, prevention of HIV transmission, and measurement of HIV incidence. We describe markers of EHI, diagnostic strategies for detecting these markers, and ways to incorporate these strategies into diagnostic and HIV incidence algorithms.

RECENT FINDINGS

For individual diagnosis in the USA and Europe, laboratory-based diagnostic algorithms increasingly incorporate fourth-generation HIV antigen tests, allowing for earlier detection. In some sub-Saharan African settings, symptom-based screening is being explored to identify subsets of persons at high risk for AHI. Point-of-care diagnostics designed for AHI detection are in the pipeline and, if validated, represent an opportunity for real-time AHI diagnosis. At the population level, multiassay algorithms are promising new strategies for estimating HIV incidence on the basis of several assays applied to cross-sectional samples. These algorithms can be developed to optimize performance, in addition to cost and logistical considerations.

SUMMARY

There are important recent advances in detection of EHIs at the individual and population levels. Applying optimal combinations of tests in diagnostic and HIV incidence algorithms is urgently needed to support the multiple goals derived from enhanced detection and discrimination of EHIs.

Performance of rapid point-of-care and laboratory tests for acute and established HIV infection in San Francisco

Background

Current laboratory and point-of-care tests for HIV detect different analytes and use different sample types. Some have fast turnaround times (<1 hour). We investigated how HIV test choice could impact case finding by testing programs.

Methods

We analyzed 21,234 consecutive HIV tests with venous blood obtained by San Francisco HIV testing programs from 2003 to 2008. For a subset, oral fluid (n = 6446) or fingerstick blood (n = 8127) samples were also obtained for rapid testing. In all cases, HIV status was determined using an HIV antibody-plus-RNA test algorithm. We assessed how the screening antibody tests performed individually versus the gold standard of the full algorithm. We then evaluated the potential ability of other tests (including new tests) to detect more cases, by re-testing all specimens that had negative/discrepant antibody results on initial screening.

Findings

The antibody-RNA algorithm identified 58 acute and 703 established HIV infection cases. 1^st-generation (Vironostika) and 3^rd-generation (Genetic Systems) immunoassays had 92 and 96 percent sensitivity, respectively. The Oraquick rapid test had clinical sensitivity of only 86 percent on oral fluid samples, but 92 percent on finger-stick blood. Newer 4^th-generation, antigen-antibody combo rapid immunoassay (ARCHITECT) detected HIV in 87 percent of all the acute cases that had been missed by one of the previous screening assays. A point-of-care 4^th generation antigen-antibody combo rapid test (Determine) detected about 54 percent of such acute cases.

Conclusions

Our study suggests that some rapid antibody blood tests will give similar case detection to laboratory antibody tests, but that oral fluid testing greatly reduces ability to detect HIV. New 4^th-generation combo tests can detect the majority of acute infections detectable by HIV RNA but with rapid results. Using these tests as a primary screening assay in high-risk HIV testing programs could reduce or eliminate the need for HIV RNA testing.

Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection in Seoul, South Korea

BACKGROUND

There have been various efforts to identify less costly but still accurate methods for monitoring the response to HIV treatment. We evaluated a pooling method to determine if this could improve screening efficiency and reduce costs while maintaining accuracy in Seoul, South Korea.

METHODS

We conducted the first prospective study of pooled nucleic acid testing (NAT) using a 5 minipool + algorithm strategy versus individual viral load testing for patients receiving antiretroviral therapy (ART) between November 2011 and August 2012 at an urban hospital in Seoul, South Korea. The viral load assay used has a lower level of detection of 20 HIV RNA copies/ml, and the cost per assay is US$ 136. The 5 minipool +algorithm strategy was applied and 43 pooled samples were evaluated. The relative efficiency and accuracy of the pooled NAT were compared with those of individual testing.

RESULTS

Using the individual viral load assay, 15 of 215 (7%) plasma samples had more than 200 HIV RNA copies/ml. The pooled NAT using the 5 minipool + algorithm strategy was applied to 43 pooled samples; 111 tests were needed to test all samples when virologic failure was defined at HIV RNA ≥ 200 copies/ml. Therefore, 104 tests were saved over individual testing, with a relative efficiency of 0.48. When evaluating costs, a total of US$ 14,144 was saved for 215 individual samples during 10 months. The negative predictive value was 99.5% for all samples with HIV RNA ≥ 200 copies/ml.

CONCLUSIONS

The pooled NAT with 5 minipool + algorithm strategy seems to be a very promising approach to effectively monitor patients receiving ART and to save resources.

Pooling strategies to reduce the cost of HIV-1 RNA load monitoring in a resource-limited setting

BACKGROUND

Quantitative human immunodeficiency virus (HIV) RNA load testing surpasses CD4 cell count and clinical monitoring in detecting antiretroviral therapy (ART) failure; however, its cost can be prohibitive. Recently, the use of pooling strategies with a clinically appropriate viral load threshold was shown to be accurate and efficient for monitoring when the prevalence of virologic failure is low.

METHODS

We used laboratory request form information to identify specimens with a low pretest probability of virologic failure. Patients aged ≥15 years who were receiving first-line ART had individual viral load results available were eligible. Blood plasma, dried blood spots, and dried plasma spots were evaluated. Two pooling strategies were compared: minipools of 5 samples and a 10 ×10 matrix platform (liquid plasma specimens only). A deconvolution algorithm was used to identify specimens(s) with detectable viral loads.

RESULTS

The virologic failure rate in the study sample was <10%. Specimens included were liquid plasma specimens tested in minipools(n = 400), of which 300 were available for testing by matrix, and specimens tested with minipools only: dried blood spots (n = 100) and dried plasma spots (n = 185). Pooling methods resulted in 30.5%-60% fewer HIV RNA tests required to screen the study sample. For plasma pooling, the matrix strategy had the better efficiency, but minipools of 5 dried blood spots had the best efficiency overall and were accurate at a >95% negative predictive value with minimal technical requirements.

CONCLUSIONS

In resource-constrained settings, a combination of preselection of patients with low pretest probability of virologic failure and pooled testing can reduce the cost of virologic monitoring without compromising accuracy.

The use of pooled viral load testing to identify antiretroviral treatment failure

BACKGROUND

To develop less costly methods to virologically monitor patients receiving antiretroviral therapy, we evaluated methods that use pooled blood samples and quantitative information available from viral load assays to monitor a cohort of patients on first-line antiretroviral therapy for virologic failure.

METHODS

We evaluated 150 blood samples collected after 6 months of therapy from participants enrolled in a San Diego primary infection program between January 1998 and January 2007. Samples were screened for virologic failure with individual viral load testing, 10 x 10 matrix pools and minipools of five samples. For the pooled platforms (matrix and minipools), we used a search and retest algorithm based on the quantitative viral load data to resolve samples that remained ambiguous for virologic failure. Viral load thresholds were more than 500 and more than 1500 copies/ml for the matrix and more than 250 and more than 500 copies/ml for the minipool. Efficiency, accuracy and result turnaround times were evaluated.

RESULTS

Twenty-three percent of cohort samples were detectable at more than 50 HIV RNA copies/ml. At an algorithm threshold of more than 500 HIV RNA copies/ml, both minipool and matrix methods used less than half the number of viral load assays to screen the cohort, compared with testing samples individually. Both pooling platforms had negative predictive values of 100% for viral loads of more than 500 HIV RNA copies/ml and at least 94% for viral loads of more than 250 HIV RNA copies/ml.

CONCLUSION

In this cohort, both pooling methods improved the efficiency of virologic monitoring over individual testing with a minimal decrease in accuracy. These methods may allow for the induction and sustainability of the virologic monitoring of patients receiving antiretroviral therapy in resource-limited settings.

Optimizing screening for acute human immunodeficiency virus infection with pooled nucleic acid amplification tests

Recent studies have shown the public health importance of identifying individuals with acute human immunodeficiency virus infection (AHI); however, the cost of nucleic acid amplification testing (NAAT) makes individual testing of at-risk individuals prohibitively expensive in many settings. Pooled NAAT (or group testing) can improve efficiency and test performance of testing for AHI, but optimizing the pooling algorithm can be difficult. We developed simple, flexible biostatistical models of specimen pooling with NAAT for the identification of AHI cases; these models incorporate group testing theory, operating characteristics of biological assays, and a model of viral dynamics during AHI. Pooling algorithm sensitivity, efficiency (test kits used per individual specimen evaluated), and positive predictive value (PPV) were modeled and compared for three simple pooling algorithms: two-stage minipools (D2), three-stage hierarchical pools (D3), and square arrays with master pools (A2m). We confirmed the results by stochastic simulation and produced reference tables and a Web calculator to facilitate pooling by investigators without specific biostatistical expertise. All three pooling strategies demonstrated improved efficiency and PPV for AHI case detection compared to individual NAAT. D3 and A2m algorithms generally provided better efficiency and PPV than D2; additionally, A2m generally exhibited better PPV than D3. Used selectively and carefully, the simple models developed here can guide the selection of a pooling algorithm for the detection of AHI cases in a wide variety of settings.

Beyond the end of exceptionalism: integrating HIV testing into routine medical care and HIV prevention

In September 2006, the US CDC issued new guidelines for HIV testing. These guidelines were designed not only to simplify and expand HIV testing but also to integrate testing into routine medical care in the USA. The nationwide implementation of these guidelines is currently facing several political and legal barriers. In this article, we examine the origins of current patient-driven and risk-based HIV testing in the USA and highlight shortcomings of this strategy. We then demonstrate how the changing HIV epidemic in the USA requires routine HIV screening at all points of contact in the medical system in order to control the HIV epidemic and how novel testing strategies could increase the yield of testing in these settings.

Diagnosis and management of acute HIV infection

HIV infection starts as an acute, systemic infection, followed by a chronic period of clinical latency, usually lasting 3 to 10 years, which precedes the eventual collapse of the immune system. It is increasingly recognized that events occurring during acute HIV infection may determine the natural course of the disease. The very dynamic events of acute HIV infection provide multiple opportunities for biologic interventions, such as anti-retroviral or immune-based therapies. Similarly, the implementation of public health measures during acute HIV infection could help control epidemics or outbreaks. Many of the dramatic possibilities for intervention in acute HIV infection remain unproved, not the least because of traditional difficulty of diagnosing patients during this early period. This article reviews the natural history, pathogenesis and clinical presentation of acute HIV infection, and suggests a diagnostic and therapeutic approach to guide clinicians dealing with patients with suspected or confirmed acute HIV infection.

Detection of acute HIV infections in an urban HIV counseling and testing population in the United States

The southeastern United States has an increasing burden of HIV, particularly among blacks, women, and men who have sex with men. To evaluate HIV nucleic acid amplification testing (NAAT) and antibody-based algorithms in determination of HIV incidence, detection of acute HIV infections, and surveillance of drug-resistant virus transmission in the urban southeastern United States, we conducted a cross-sectional analysis of prospectively collected data from 2202 adults receiving HIV testing and counseling at 3 sites in Atlanta, GA from October 2002 through January 2004. After standard testing with an HIV enzyme immunoassay (EIA) and Western blot confirmation, HIV-positive specimens were tested with 2 standardized assays to detect recent infection. HIV antibody-negative specimens were pooled and screened for HIV using NAAT. Seventy (3.2%) of 2202 subjects were HIV infected. Only 66 were positive on the standard HIV antibody test; 4 were antibody-negative but acutely HIV infected. The overall annual HIV incidence was 1.1% (95% confidence interval [CI]: 0.4 to 1.8) based on the Vironostika-LS assay and 1.3% (95% CI: 0.6 to 2.1) based on the BED Incidence Enzyme Immunoassay (EIA). The prevalence of acute HIV infection was 1.8 per 1000 persons (95% CI: 0.7 to 4.6). The sensitivity of the current testing algorithm using an EIA and Western blot test for detectable infections was only 94.3% (95% CI: 86.2 to 97.8). All 3 of the acutely infected subjects genotyped had drug resistance mutations, and 1 had multiclass resistance. Adding NAAT-based screening to standard HIV antibody testing increased case identification by 6% and uncovered the first evidence of multidrug-resistant HIV transmission in Atlanta. Antibody tests alone are insufficient for public health practice in high-risk urban HIV testing settings.

Characteristics of persons with recently acquired HIV infection: application of the serologic testing algorithm for recent HIV seroconversion in 10 US cities

BACKGROUND

Information about the characteristics of persons whose HIV diagnosis was made soon after infection contributes to a better understanding of the HIV epidemic and to appropriate targeting of care and prevention efforts.

METHODS

In 10 US cities from 1997 through 2001, specimens from consenting persons for whom a diagnosis of HIV was made within the past 12 months in were tested using the serologic testing algorithm for recent HIV seroconversion. The characteristics of those whose HIV diagnosis occurred within 170 days (on average) from seroconversion were identified.

RESULTS

For 191 (20%) of the 964 participants, an HIV diagnosis was made during the period of recent infection. These diagnoses of recent infection were made more frequently among men (21.7%), whites (29.3%), men who have sex with men (25.5%), persons with a known HIV-infected partner (24.9%), and persons with a diagnosis of gonorrhea made in the 12 months before interview (27.0%). Recent infection was diagnosed less frequently among African Americans (15.5%), Latinos (15.5), and heterosexual men (14.7%) and women (14.4%).

CONCLUSIONS

To increase early diagnosis of HIV, HIV testing should be more routinely offered to persons with a recent history of sexually transmitted diseases and to African Americans and Latinos in a variety of settings.

Approaching "HIV elimination": Interventions for acute HIV infection

Recent observations from several groups suggest that individuals with acute (antibody negative) HIV infections (AHI) may present for "routine" HIV testing in unanticipated numbers. Most of these papers have highlighted the use of group testing strategies to screen antibody negative testing sera for HIV RNA using nucleic acid amplification tests. At the same time, accumulating evidence indicates that AHI is a time of briefly, but substantially elevated risk for transmission of HIV. In this paper, we review these new data with attention to their implications for HIV prevention strategies. By calling attention to a subset of patients that are both recently infected and at transiently very high risk of transmitting their new infection to partners, AHI detection makes it possible to use traditional, network notification-based public health strategies effectively in the fight against HIV.

Primary HIV Infection Education

BACKGROUND

Although many individuals who acquire HIV are symptomatic, primary HIV infection (PHI) is infrequently diagnosed, even after the integration of RNA testing into HIV screening programs. Until more individuals with PHI seek evaluation, the public health impact of RNA testing is likely to be small.

OBJECTIVE

To describe knowledge of PHI and attitudes toward health care-seeking behavior for symptoms consistent with PHI in men who have sex with men (MSM).

METHODS

Between April 2004 and March 2005, HIV-negative MSM attending the Public Health-Seattle and King County sexually transmitted disease (STD) clinic completed an anonymous, self-administered, written questionnaire.

RESULTS

Ninety-six (64%) of 150 subjects named > or =1 symptom associated with PHI. Only 18 (39%) of 46 men who knew PHI could resemble influenza would seek care for flu-like symptoms. Fifteen (65%) of 23 men reporting a week-long febrile illness with rash in the preceding year sought health care, but only 7 (30%) were tested for HIV.

CONCLUSIONS

Although most subjects identified some symptoms of PHI, relatively few would seek care for such symptoms. MSM seeking attention for febrile illnesses were infrequently tested for HIV. Increased symptom recognition, health care-seeking behavior, and routine HIV RNA testing are needed if PHI screening programs are to have meaningful impact.